Package Bio :: Package Sequencing :: Module Phd
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Module Phd

source code

Parser for PHD files output by PHRED and used by PHRAP and CONSED.

This module can be used directly which will return Record objects which should contain all the original data in the file.

Alternatively, using Bio.SeqIO with the "phd" format will call this module internally. This will give SeqRecord objects for each contig sequence.

Classes [hide private]
  Record
Hold information from a PHD file.
Functions [hide private]
 
read(handle)
Reads the next PHD record from the file, returning it as a Record object.
source code
 
parse(handle)
Iterates over a file returning multiple PHD records.
source code
Variables [hide private]
  CKEYWORDS = ['CHROMAT_FILE', 'ABI_THUMBPRINT', 'PHRED_VERSION'...
  __package__ = 'Bio.Sequencing'
Function Details [hide private]

read(handle)

source code 

Reads the next PHD record from the file, returning it as a Record object.

This function reads PHD file data line by line from the handle, and returns a single Record object.

parse(handle)

source code 

Iterates over a file returning multiple PHD records.

The data is read line by line from the handle. The handle can be a list of lines, an open file, or similar; the only requirement is that we can iterate over the handle to retrieve lines from it.

Typical usage:

records = parse(handle)
for record in records:
    # do something with the record object

Variables Details [hide private]

CKEYWORDS

Value:
['CHROMAT_FILE',
 'ABI_THUMBPRINT',
 'PHRED_VERSION',
 'CALL_METHOD',
 'QUALITY_LEVELS',
 'TIME',
 'TRACE_ARRAY_MIN_INDEX',
 'TRACE_ARRAY_MAX_INDEX',
...